BN1339 Genetic Spatial Mapping Report

Genetic Spatial Mapping Plot

This plot shows the spatial genetic mapping results across different tissues.

Cauchy Combination Result

This table presents the results of the Cauchy combination test, summarizing the genetic associations.

Annotation P Cauchy P Median
Layer 4 4.4394e-05 3.6008e-03
Layer 5 1.9048e-04 5.5204e-03
Layer 3 4.3855e-04 8.0477e-03
Layer 6 8.2297e-04 2.7219e-02
WM 1.1348e-01 2.1679e-01
Layer 2 4.6767e-01 5.8759e-01

Diagnosis Manhattan Plot

The Manhattan plot shows the association of SNPs with the top associated gene across the genome.

Gene Expression and GSS Distribution

Select a gene to view its expression distribution and gene specificity score (GSS).

Expression Distribution
SNCA Expression Distribution
Gene Specificity Score (GSS)
SNCA GSS Distribution

Top 50 Gene Diagnostic Info

This table lists the top 50 genes based on diagnostic criteria, including the gene specificity score (GSS) and PCC.

Gene Annotation Median GSS PCC
SNCA Layer 6 2.1055 0.6369
CHGA Layer 4 2.2969 0.5796
PNMA8A Layer 4 2.1348 0.5737
TUBA4A Layer 4 2.2871 0.5708
PFKP Layer 5 2.3027 0.5627
RNPS1 Layer 4 2.1797 0.5607
AMPH Layer 4 2.1621 0.5560
PSMB4 Layer 4 1.9053 0.5556
PREPL Layer 4 2.0781 0.5540
CAB39 Layer 4 1.9629 0.5525
TTC9B Layer 4 2.1387 0.5509
SH3GL2 Layer 4 2.2002 0.5503
ATP1A3 Layer 3 2.0781 0.5497
SYN2 Layer 5 2.1621 0.5467
SUMO1 Layer 4 2.0449 0.5451
SYNGR1 Layer 4 2.2744 0.5440
SERPINI1 Layer 4 2.1152 0.5435
SLC12A5 Layer 4 2.3926 0.5427
NPDC1 Layer 3 2.0625 0.5411
MLLT11 Layer 5 2.0684 0.5396
GABARAPL1 Layer 4 2.1602 0.5384
EEF1A2 Layer 4 2.0723 0.5380
SULT4A1 Layer 4 2.2832 0.5376
FAM49A Layer 4 2.1699 0.5374
STMN3 Layer 3 2.0723 0.5373
DIRAS1 Layer 4 2.2227 0.5351
SNCG Layer 3 2.2871 0.5348
SPRYD3 Layer 5 2.0625 0.5337
EIF5 Layer 4 1.9878 0.5335
GABRG2 Layer 4 2.2266 0.5330
ELMOD1 Layer 4 2.0625 0.5326
MYO5A Layer 4 2.1445 0.5319
AP2M1 Layer 5 1.8965 0.5313
FXYD6 Layer 4 2.1191 0.5313
CAMK2G Layer 4 2.1250 0.5312
SMYD2 Layer 5 2.1973 0.5311
INPP5F Layer 4 2.2373 0.5311
PAK1 Layer 4 2.2773 0.5305
NCKAP1 Layer 4 2.1543 0.5302
ANK2 Layer 4 2.0684 0.5300
PNMA2 Layer 4 2.1777 0.5299
GABRA1 Layer 3 2.0176 0.5294
GLUD1 Layer 3 1.9990 0.5292
HCFC1R1 Layer 3 1.9766 0.5289
WBP2 Layer 4 2.0391 0.5284
ATP5MD Layer 5 1.9189 0.5279
MAPRE3 Layer 4 2.2168 0.5276
ACTR1B Layer 4 1.9189 0.5276
CD200 Layer 4 2.1777 0.5264
S100A6 Layer 4 1.9053 0.5255

Running Info

Click to view detailed run information and parameters.

gsMap Version: 1.73.0

Parameters:

  • Sample Name: BN1339
  • Trait Name: PD
  • Summary Statistics File: /mnt/data/projects/ASAP/ST/gsMAP/GWAS_nallsEtAl2019_allSamples_allVariants.sumstats.gz
  • HDF5 Path: /mnt/data/projects/ASAP/ST/gsMAP/st_anndata_h5ads/st_adata_BN1339_for_gsmap.h5ad
  • Annotation: smoothed_label_s5
  • Spatial LDSC Save Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1339/spatial_ldsc
  • Cauchy Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1339/cauchy_combination
  • Report Directory: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1339/report/PD
  • gsMap Report File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1339/report/PD/BN1339_PD_gsMap_Report.html
  • Gene Diagnostic Info File: /mnt/data/projects/ASAP/ST/gsMAP/st_mtg_out/BN1339/report/PD/BN1339_PD_Gene_Diagnostic_Info.csv
  • Report Generation Date: 2025-04-11 03:29:26
  • Number of Processes: 10
  • Spending Time: 0h 2m